SMTL ID : 7w3i.1

Structure of USP14-bound human 26S proteasome in substrate-inhibited state SB_USP14

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-1-1-1-2-2-2-2-2-2-2-2-2-2-2-2-2-2-1-1-1-1-1-1-1-1-1-1-1-1-1-mer

Ligands

4 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.1: 20 residues within 4Å: Chain B: D.176, V.177, G.178, P.218, G.219, T.220, G.221, K.222, T.223, L.224, E.276, N.322, I.354, H.358, G.382, A.383, R.386 Chain C: D.317, G.318, R.343 14 PLIP interactions: 9 interactions with chain B, 5 interactions with chain C Hydrogen bonds: B:G.178, B:G.221, B:K.222, B:T.223, B:T.223, B:L.224, B:N.322, B:G.382, C:D.317, C:R.343 Salt bridges: B:K.222, C:R.343, C:R.343, C:R.343 ATP.4: 18 residues within 4Å: Chain E: I.167, G.168, P.208, G.209, C.210, G.211, K.212, T.213, M.214, E.266, N.312, I.344, I.348, G.372, A.373, N.376 Chain F: R.305, R.308 20 PLIP interactions: 16 interactions with chain E, 4 interactions with chain F Hydrogen bonds: E:G.168, E:G.168, E:G.209, E:C.210, E:C.210, E:K.212, E:T.213, E:T.213, E:M.214, E:E.266, E:E.266, E:N.312, E:N.312, E:A.373, E:N.376 Salt bridges: E:K.212, F:R.305, F:R.305, F:R.305, F:R.308 ATP.5: 21 residues within 4Å: Chain F: E.148, I.149, G.150, P.189, P.190, G.191, T.192, G.193, K.194, T.195, L.196, D.247, N.294, I.326, H.330, G.354, A.355, R.358 Chain G: D.318, R.344, R.347 17 PLIP interactions: 13 interactions with chain F, 4 interactions with chain G Hydrogen bonds: F:G.150, F:G.150, F:G.191, F:T.192, F:G.193, F:K.194, F:T.195, F:T.195, F:L.196, F:N.294, F:N.294 Salt bridges: F:K.194, F:K.194, G:R.344, G:R.344, G:R.344, G:R.347 ATP.6: 18 residues within 4Å: Chain B: R.333, R.336 Chain G: I.188, G.189, P.229, G.230, T.231, G.232, K.233, T.234, L.235, E.287, N.333, I.365, H.369, G.393, A.394, K.397 12 PLIP interactions: 7 interactions with chain G, 5 interactions with chain B Hydrogen bonds: G:G.189, G:G.232, G:K.233, G:T.234, G:E.287, G:N.333, G:N.333 Salt bridges: B:R.333, B:R.333, B:R.333, B:R.336, B:R.336

2 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.2: 15 residues within 4Å: Chain C: I.187, G.188, P.228, G.229, T.230, G.231, K.232, T.233, L.234, I.364, H.368, G.392, A.393, K.396 Chain D: R.299 9 PLIP interactions: 8 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:G.188, C:G.229, C:G.231, C:K.232, C:T.233, C:L.234 Salt bridges: C:K.232, C:K.232, D:R.299 ADP.3: 13 residues within 4Å: Chain D: I.143, P.183, P.184, G.185, T.186, G.187, K.188, T.189, L.190, I.320, H.324, A.349, K.352 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:I.143, D:P.183, D:G.185, D:T.186, D:K.188, D:T.189, D:L.190 Salt bridges: D:K.188

1 x ZN: ZINC ION(Non-covalent)

ZN.7: 4 residues within 4Å: Chain i: H.113, H.115, L.122, D.126 4 PLIP interactions: 4 interactions with chain i Metal complexes: i:H.113, i:H.115, i:D.126, i:D.126

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, S. et al., USP14-regulated allostery of the human proteasome by time-resolved cryo-EM. Nature (2022)

Release Date

2022-05-18

Peptides

Ubiquitin carboxyl-terminal hydrolase 14: A
26S protease regulatory subunit 7: B
26S protease regulatory subunit 4: C
Isoform 2 of 26S proteasome regulatory subunit 8: D
26S protease regulatory subunit 6B: E
26S proteasome regulatory subunit 10B: F
26S protease regulatory subunit 6A: G
Proteasome subunit alpha type-6: HV
Proteasome subunit alpha type-2: IW
Proteasome subunit alpha type-4: JX
Proteasome subunit alpha type-7: KY
Proteasome subunit alpha type-5: LZ
Isoform Long of Proteasome subunit alpha type-1: M0
Proteasome subunit alpha type-3: N1
Proteasome subunit beta type-6: O2
Proteasome subunit beta type-7: P3
Proteasome subunit beta type-3: Q4
Proteasome subunit beta type-2: R5
Proteasome subunit beta type-5: S6
Proteasome subunit beta type-1: T7
Proteasome subunit beta type-4: U8
Ubiquitin: 9
26S proteasome non-ATPase regulatory subunit 1: a
26S proteasome non-ATPase regulatory subunit 3: b
26S proteasome non-ATPase regulatory subunit 12: c
26S proteasome non-ATPase regulatory subunit 11: d
26S proteasome non-ATPase regulatory subunit 6: e
26S proteasome non-ATPase regulatory subunit 7: f
26S proteasome non-ATPase regulatory subunit 13: g
26S proteasome non-ATPase regulatory subunit 4: h
26S proteasome non-ATPase regulatory subunit 14: i
26S proteasome non-ATPase regulatory subunit 8: j
26S proteasome non-ATPase regulatory subunit 2: k
26S proteasome complex subunit DSS1: l

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
x

B
A

C
B

D
C

E
D

F
E

G
F

H
G

V
g

I
H

W
h

J
I

X
i

K
J

Y
j

L
K

Z
k

M
L

0
l

N
M

1
m

O
N

2
n

P
O

3
o

Q
P

4
p

R
Q

5
q

S
R

6
r

T
S

7
s

U
T

8
t

9
y

a
U

b
V

c
W

d
X

e
Y

f
Z

g
a

h
b

i
c

j
d

k
f

l
e

Ubiquitin carboxyl-terminal hydrolase 14

26S protease regulatory subunit 7

26S protease regulatory subunit 4

Isoform 2 of 26S proteasome regulatory subunit 8

26S protease regulatory subunit 6B

26S proteasome regulatory subunit 10B

26S protease regulatory subunit 6A

Proteasome subunit alpha type-6

Proteasome subunit alpha type-2

Proteasome subunit alpha type-4

Proteasome subunit alpha type-7

Proteasome subunit alpha type-5

Isoform Long of Proteasome subunit alpha type-1

Proteasome subunit alpha type-3

Proteasome subunit beta type-6

Proteasome subunit beta type-7

Proteasome subunit beta type-3

Proteasome subunit beta type-2

Proteasome subunit beta type-5

Proteasome subunit beta type-1

Proteasome subunit beta type-4

Ubiquitin

26S proteasome non-ATPase regulatory subunit 1

26S proteasome non-ATPase regulatory subunit 3

26S proteasome non-ATPase regulatory subunit 12

26S proteasome non-ATPase regulatory subunit 11

26S proteasome non-ATPase regulatory subunit 6

26S proteasome non-ATPase regulatory subunit 7

26S proteasome non-ATPase regulatory subunit 13

26S proteasome non-ATPase regulatory subunit 4

26S proteasome non-ATPase regulatory subunit 14

26S proteasome non-ATPase regulatory subunit 8

26S proteasome non-ATPase regulatory subunit 2

26S proteasome complex subunit DSS1

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